Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Sandification vs. muddification of tidal flats by benthic organisms: A flume study
Soissons, Laura M. ; Gomes da Conceiçâo, Tatiana ; Bastiaan, John ; Dalen, Jeroen van; Ysebaert, Tom ; Herman, Peter M.J. ; Cozzoli, Francesco ; Bouma, Tjeerd J. - \ 2019
Estuarine Coastal and Shelf Science 228 (2019). - ISSN 0272-7714
Benthic organisms - Cerastorderma edule - Ruditapes philippinarum - Sediment properties - Silt content - Suspended sediment concentration - Tidal flats

Bioturbating benthic organisms have typically been characterised by how they modify the vertical sediment erosion thresholds. By means of several annular flume experiments, we aimed to understand how benthic organisms may affect grain-size sediment properties over time, and how this depends on the sediment type and the sediment loading of the water column. We compared the effect of two bioturbating macroinvertebrate species: a local dominant species, the cockle Cerastoderma edule and a spreading non-indigeneous species, the clam Ruditapes philippinarum. Our results indicate that the effect of benthic organisms on sediment dynamics is strongly dependent on both the prevailing environmental conditions and the benthic species present. If sediment is sandy, the benthos can gradually enhance the silt content of the sediment by mixing in part of the daily tidal sediment deposition. In contrast, if sediment is muddy, benthos can gradually decrease the silt content of the sediment by specifically suspending the fine fraction. Moreover, we observed that the native cockles had a stronger impact than invasive clams. Therefore, bioturbating benthos can have an important effect in determining the local sediment properties, with the outcome depending both on the species in question and the environmental conditions the bioturbator lives in. Our findings show that sediment bioturbation may have strong implications for tidal flat stability undergoing major changes from natural or anthropogenic sources.

Mussel seed is highly plastic to settling conditions: the influence of waves versus tidal emergence
Schotanus, J. ; Capelle, J. ; Leuchter, L. ; Koppel, J. van de; Bouma, T.J. - \ 2019
Marine Ecology Progress Series 624 (2019). - ISSN 0171-8630 - p. 77 - 87.
Phenotypic plasticity - Phenotypic adjustment - Intertidal hydrodynamic conditions - Transplantation
Phenotypic plasticity is important for organisms to adjust to a new environment.
Therefore, the transplantation success of an organism to a new environment can be increased with knowledge of its capacity for phenotypic plasticity in different life stages, and the phenotypic adjustments it needs to make in specific environmental situations. Both the capacity for phenotypic plasticity and the necessary phenotypic adjustments for transplantation were tested in a mesocosm experiment using blue mussels Mytilus edulis as a model organism. This study tested (1) to what extent mussel seed coming from collectors in the water column are still capable of adjusting their phenotype, and (2) whether exposure to air or wave action is more important as a driver of phenotypic adjustments for mussels living in intertidal conditions. We found that mussel
seed had a high capacity for phenotypic plasticity, and were capable of adjusting their morphology to accommodate different intertidal hydrodynamic conditions. Exposure to air influenced the shell shape, condition, byssal attachment strength and aggregation behaviour, but exposure to waves played the most important role in determining the phenotype of mussels. Wave-exposed
mussels grew bigger, rounder, had thicker shells and a stronger byssal attachment strength than mussels exposed to either calm tidal or calm submerged environments. This knowledge is important for selecting a suitable source population and transplantation location.
Putting self‐organization to the test: labyrinthine patterns as optimal solution for persistence
Bertolini, Camilla ; Cornelissen, Brenda ; Capelle, Jacob ; De Koppel, Johan Van; Bouma, Tjeerd J. - \ 2019
Oikos (2019). - ISSN 0030-1299 - 11 p.
benthic dynamics - density-dependent - facilitation - habitat complexity - mussel beds - Self-organization
Spatial patterns formed through the process of self-organization are found in nature across a variety of ecosystems. Pattern formation may reduce the costs of competition while maximizing the benefits of group living, and thus promote ecosystem persistence. This leads to the prediction that self-organizing to obtain locally intermediate densities will be the optimal solution to balance costs and benefits. However, despite much evidence documenting pattern formation in natural ecosystems, there is limited empirical evidence of how these patterns both influence and are influenced by tradeoffs between costs and benefits. Using mussels as a model system, we coupled field observations in mussel-culture plots with manipulative laboratory experiments to address the following hypotheses: 1) labyrinthine spatial patterns, characteristically found at intermediate to high patch densities, are the most persistent over time; this
is because labyrinthine patterns 2) result in adequately heavy patches that can maximize resistance to dislodgement while 3) increasing water turbulence with spacing, which will maximize food delivery processes. In the field, we observed that labyrinthine ‘stripes’ patterns are indeed the most persistent over time, confirming our first hypothesis. Furthermore, with laboratory experiments, we found the ‘stripes’ pattern to be highly resistant to dislodgement, confirming the second hypothesis. Finally, with regards to the third hypothesis, we found positive effects of this pattern on local turbulence. These results suggest that the mechanisms of intraspecific facilitation not only depend on initial organism densities, but may also be influenced by spatial patterning. We hence recommend taking into account spatial patterns to maximize productivity
and persistence in shellfish-cultivation practices and to increase the restoration success of ecosystems with self-organizing properties.
Nederland anno 2045: een landschap van masten en exoten
Berendse, Frank ; Schaminee, Joop ; Putten, Wim van der - \ 2019
Professor Wageningen: ‘Zeg sorry, universiteit’
Turnhout, Esther ; Vink, Simon - \ 2019
ICON.NL: coastline observatory to examine coastal dynamics in response to natural forcing and human interventions
Aarninkhof, Stefan ; Schipper, Matthieu De; Luijendijk, Arjen ; Ruessink, Gerben ; Bierkens, Marc ; Wijnberg, Kathelijne ; Roelvink, Dano ; Limpens, J. ; Baptist, M.J. ; Riksen, Michel ; Bouma, Tjeerd ; Vries, Sierd de; Reniers, Ad ; Hulscher, Suzanne ; Wijdeveld, Arjan ; Dongeren, Ap van; Gelder-Maas, Carola van; Lodder, Quirijn ; Spek, Ad van der - \ 2019
- 8 p.
In the light of challenges raised by a changing climate and increasing population pressure in coastal regions, it has become clear that theoretical models and scattered experiments do not provide the data we urgently need to understand coastal conditions and processes. We propose a Dutch coastline observatory named ICON.NL, based at the Delfland Coast with core observations focused on the internationally well-known Sand Engine experiment, as part of an International Coastline Observatories Network (ICON). ICON.NL will cover the physics and ecology from deep water to the dunes. Data will be collected continuously by novel remote sensing and in-situ sensors, coupled to numerical models to yield unsurpassed long-term coastline measurements. The combination of the unique site and ambitious monitoring design enables new avenues in coastal science and a leap in interdisciplinary research.
Financieringsbehoefte natuurinclusieve landbouw : rapportage eerste fase: beschrijvende analyse vragenlijst / Jetske Bouma, Mark Koetse, Nico Polman; met dank aan Jeroen Brandsma : Rapportage eerste fase: beschrijvende analyse vragenlijst / Jetske Bouma, Mark Koetse, Nico Polman; met dank aan Jeroen Brandsma
Bouma, Jetske ; Koetse, Mark ; Polman, Nico ; Brandsma, Jeroen - \ 2019
Den Haag : PBL Planbureau voor de Leefomgeving - 73
Creating a window of opportunity for establishing ecosystem engineers by adding substratum: a case study on mussels
Capelle, Jacob J. ; Leuchter, Lennet ; Wit, Maurice ; Hartog, Eva ; Bouma, Tjeerd J. - \ 2019
Ecosphere 10 (2019)4. - ISSN 2150-8925 - p. e02688 - e02688.
aggregation - Density dependence - dislodgement - disturbance - flume - Mytilus edulis - positive feedback - stable state
Ecosystem engineers typically exert positive feedback on their environment, which enhances their performance. Such positive feedback is lacking in the establishment phase, when densities are too low and/or patches are too small. There is a strong need to unravel the mechanisms for overcoming the resulting
establishment thresholds, both for ecological restoration purposes and to be able to use their services. In the present study, we question whether providing a transient substratum can be used as tool to overcome establishment thresholds, by creating a window of opportunity for initial settlement, using mussels (Mytilus edulis) as a model system. Combining field and flume experiments, we study how biogenic substratum enrichment in the form of a shell layer on a soft mudflat affects the critical dislodgement thresholds and, thus, the chances of mussel establishment at different mussel densities and aggregation states. Flume results showed that the presence of a shell layer reduced dislodgement of mussel patches in low-energy environments but was conditional for establishment in high-energy environments. That is, in high-energy environments with shells, aggregation into clumps enhanced dislodgement, while dislodgement was reduced with increasing overall mussel biomass and overall mussel patch weight. Without shells, dislodgement was always 100%. These findings agreed with our field studies, which showed that coarse shell material reduced mussel losses (by a factor of 3), reduced aggregation (by a factor of 2.4), and increased attachment strength (by a factor of 2.4). Overall, our results show that the local presence of biogenic substratum increases the
chance of mussel establishment by enhancing the critical hydrodynamic dislodgement threshold. Thus, the local addition of a biogenic substratum may create a window of opportunity to initiate settlement in more
dynamic environments, to shift at a local scale from a bare mudflat state into an established biogenic reef state. Our findings have clear implications for how to approach restoration and management of ecosystem engineers dominated systems. For instance, when positive feedback of ecosystem engineers is lacking, (1) the transient offering of suitable settling substratum may be a necessary step to overcome establishment thresholds, and (2) this becomes increasingly important with increasing abiotic stress.
A process based model of cohesive sediment resuspension under bioturbators’ influence
Cozzoli, Francesco ; Gjoni, Vojsava ; Pasqua, Michela Del; Hu, Zhan ; Ysebaert, Tom ; Herman, Peter M.J. ; Bouma, Tjeerd J. - \ 2019
Science of the Total Environment 670 (2019). - ISSN 0048-9697 - p. 18 - 30.
Annular flumes - Bioturbation - Metabolism - Process-based model - Sediment resuspension

Macrozoobenthos may affect sediment stability and erodibility via their bioturbating activities, thereby impacting both the short- and long-term development of coastal morphology. Process-based models accounting for the effect of bioturbation are needed for the modelling of erosion dynamics. With this work, we explore whether the fundamental allometric principles of metabolic activity scaling with individual and population size may provide a framework to derive general patterns of bioturbation effect on cohesive sediment resuspension. Experimental flumes were used to test this scaling approach across different species of marine, soft-sediment bioturbators. The collected dataset encompasses a range of bioturbator functional diversity, individual densities, body sizes and overall population metabolic rates. Measurements were collected across a range of hydrodynamic stress from 0.02 to 0.25 Pa. Overall, we observed that bioturbators are able to slightly reduce the sediment resuspension at low hydrodynamic stress, whereas they noticeably enhance it at higher levels of stress. Along the whole hydrodynamic stress gradient, the quantitative effect of bioturbators on sediment resuspension can be efficiently described by the overall metabolic rate of the bioturbating benthic communities, with significant variations across the bioturbators’ taxonomic and functional diversity. One of the tested species (the gallery-builder Polychaeta Hediste diversicolor) had an effect that was partially deviating from the general trend, being able to markedly reduce sediment resuspension at low hydrodynamic stress compared to other species. By combining bioturbators’ influence with hydrodynamic force, we were able to produce a process-based model of biota-mediated sediment resuspension.

Timing it right: Non-consumptive effects on prey recruitment magnify overtime
Bertolini, C. ; Capelle, J.J. ; Timmermans, K. ; Bouma, T.J. ; De Koppel, J. Van; Derksen, G.C.H. - \ 2019
Journal of Experimental Marine Biology and Ecology 513 (2019). - ISSN 0022-0981 - p. 47 - 54.
Predator-prey - Indirect interactions - Population dynamics - Benthic ecology - Mytilus edulis - Asterias rubens
Many organisms rely on chemical signals and cues to determine habitat suitability and safety. Chemical signals can mediate many interactions, including those between predators and their prey. Altering prey behaviour, these non-consumptive effects (NCEs) can influence population and community dynamics. Understanding how NCEs influence early life history stages, such as ‘decisions’ of benthic species with planktonic larvae about where to settle, can provide useful information on the ecological functioning of these systems as well as the management for commercial usage, although most studies have so far focused on intertidal systems which are already subject to a set of stressful conditions. With a shallow subtidal field experiment we investigated NCEs of the common starfish Asterias rubens on one of its main preys, the blue mussels Mytilus edulis. We tested the hypotheses that (1) the presence of starfish reduces mussels settlement and that (2) the mussels that settle will invest more energy towards induced defences than to growth, and will thus remain smaller than mussels settling in an area without starfish. Two independent trials revealed a significant reduction of mussel spat on the collectors in the presence of starfish after a two-week deployment period. There was however no effect of starfish on the size distribution of the mussel spat. The delayed observation of effects of starfish, absent after the first week but evident afterwards, suggests a time dependency of NCE's on spat settlement. Harnessing this ecologically important information has the potential to increase yield of mussel seeds available for fisheries by either removing starfish from the ground-based settling areas at the onset and for the duration of spatfall or by using floating substrates that are away from the bottom-bound starfish. Moreover, these results also underlines the potential of using predator cues in the application for sustainable natural antifouling compounds in situations with low recruitment pressures.
An integral approach to design the Roggenplaat intertidal shoal nourishment
Werf, J.J. van der; Vet, P.L.M. de; Boersema, M.P. ; Bouma, T.J. ; Nolte, A.J. ; Schrijvershof, R.A. ; Soissons, L.M. ; Stronkhorst, J. ; Zanten, E. van; Ysebaert, T. - \ 2019
Ocean & Coastal Management 172 (2019). - ISSN 0964-5691 - p. 30 - 40.
Estuarine management - Intertidal shoal - Morphological modelling - Sediment nourishment design

The Eastern Scheldt, a tidal basin in the southwest of The Netherlands, underwent large physical and ecological changes due to a system-wide human interference. The construction of a storm surge barrier at the seaward side and closure of the upstream branches in the 1980s resulted in intertidal flat erosion. This has far reaching consequences for the ecological functioning of these habitats, especially as foraging ground for many wader species. Therefore, a 1.3 million m3 sand nourishment is foreseen on the Roggenplaat intertidal shoal to mitigate the erosion and preserve suitable foraging habitat for waders for the coming 25 years. This paper presents an integral nourishment design approach. It consists of the following steps: (i) understanding the morphology and ecology, (ii) translation of the nourishment objective into an evaluation framework, (iii) construction of a suitability map indicating potential nourishment locations, (iv) generation of nourishment designs, (v) short-term morphodynamic numerical model simulations, (vi) estimation of the long-term shoal development using a simplified approach, (vii) integral evaluation leading to the preferred design. This integral approach resulted in a design that is expected to fulfill the Roggenplaat nourishment objective, accounting for ecological, morphological, economical and technical aspects. This integrated approach could form a basis for future intertidal shoal nourishment designs worldwide.

Heeft de sterfte van zeekoeten op de Noordzee te maken met de gezonken containers?
Leopold, Mardik - \ 2019
Overdosis zonnebrandcrème funest voor koraal rond Bonaire
Slijkerman, Diana - \ 2019
Dog-directed parenting as a candidate determinant of dog to owner attachment
Bouma, K. ; Herwijnen, Ineke van; Beerda, B. - \ 2018
In: Proceedings of the ISAE Benelux conference 2018. - International Society for Applied Ethology (ISAE) - p. 20 - 20.
Attachment between dog and owner should establish that the owner acts as a secure base from which the dog can freely explore and interact with the environment. Insecure attachment may cause problem behaviour and poor welfare, and is possibly prevented by appropriate dog-directed parenting. Recently, we identified three dog-directed parenting styles, which were authoritarian correction oriented (AUN), authoritative training oriented (AUT) and authoritative intrinsic value oriented (AUI). We studied how these styles associate with dog to owner attachment as measured with a Strange Situation Test (SST) protocol with different test episodes. In these episodes the dog was either alone in an unfamiliar room, with a stranger, the owner or both. Dog behaviours were grouped by principal component analysis (PCA). Online questionnaires were used to calculate owner-report based scores for parenting styles and these were related to SST dog behaviour scores, as grouped in the PCA. A preliminary analysis of 35 dog-owner dyads correlated AUT dog-directed parenting to behaviours indicative of secure attachment (N=35, r=0.38, p=0.025), which included dogs exploring more during owner presence. Insecure attachment scores were also derived from PCA, and included behaviours such as vocalisations during owner absence. These scores correlated negatively with AUN parenting (N=35, r=-0.48, p=0.004) and positively with AUI parenting (N=35, r=0.46, p=0.006). Our preliminary findings are in agreement with what is known about the parent-child bond, suggesting that for dogs the authoritarian parenting style is most optimal as it is for children. Though the causality of dog-directed parenting and dog to owner attachment remains to be evidenced. Here we find that dog-directed parenting styles may be a route for facilitating appropriate dog to owner attachment and thereby protects dogs from negative emotional states and impaired welfare.
Oesterdam sand nourishment : Ecological and morphological development of a local sand nourishment
Boersema, Matthijs P. ; Werf, Jebbe van der; Salvador de Paiva, João N. ; Brink, Anneke M. van den; Soissons, Laura ; Walles, Brenda ; Bouma, Tjeerd J. ; Vet, P.L.M. de; Ysebaert, Tom J.W. ; Paree, Edwin ; Bijleveld, Mariska ; Zanten, Eric van; Westenbrugge, Kees van; Stronkhorst, Joost ; Jong, Dick de - \ 2018
Vlissingen : Centre of Expertise Delta Technology - 78
Boer wil verduurzamen om uit de crisis te komen
Wiskerke, Han - \ 2018

De Staat van de Boer; de agrarische sector is dringend toe aan een andere koers. Wat blijkt: boeren willen best veranderen en vergroenen, als er tenminste duidelijkhedi komt in het beleid.

Het Boerenland smacht naar een visionair
Wiskerke, Han - \ 2018

Volgens De Wageningse hoogleraar Han Wiskerke de uitkomsten van 'De Staat van de Boer'vooral kansen voor een structurele hervorming van de agrarische sector. Maar dan moet er nu wel iemand met een heldere toekomstvisie opstaan.

Exploring contacts facilitating transmission of influenza A(H5N1) virus between poultry farms in West Java, Indonesia : A major role for backyard farms?
Wibawa, Hendra ; Karo-Karo, Desniwaty ; Pribadi, Eko Sugeng ; Bouma, Annemarie ; Bodewes, Rogier ; Vernooij, Hans ; Diyantoro, ; Sugama, Agus ; Muljono, David H. ; Koch, Guus ; Tjatur Rasa, Fadjar Sumping ; Stegeman, Arjan - \ 2018
Preventive Veterinary Medicine 156 (2018). - ISSN 0167-5877 - p. 8 - 15.
Avian influenza - Contact structure - H5N1 - Indonesia - Poultry - Transmission
Highly pathogenic avian influenza virus (HPAIV) H5N1 has been reported in Asia, including Indonesia since 2003. Although several risk factors related to the HPAIV outbreaks in poultry in Indonesia have been identified, little is known of the contact structure of farms of different poultry production types (backyard chickens, broilers, layers, and ducks). This study aims to quantify the contact rates associated with the movement of people, and movements of live birds and products and equipment that affect the risk of HPAIV H5N1 transmission between poultry farms in Indonesia. On 124 poultry farms in 6 districts in West Java, logbooks were distributed to record the movements of farmers/staff and visitors and their poultry contacts. Most movements in backyard chicken, commercial native chicken, broiler and duck farms were visits to and from other poultry farms, whilst in layer farms visits to and from poultry companies, visits to egg collection houses and visit from other poultry farms were most frequent. Over 75% of persons visiting backyard chicken and duck farms had previously visited other poultry farms on the same day. Visitors of backyard chicken farms had the highest average contact rate, either direct contact with poultry on other farms before the visits (1.35 contact/day) or contact during their visits in the farms (10.03 contact/day). These results suggest that backyard chicken farms are most at risk for transmission of HPAIV compared to farms of the other poultry production types. Since visits of farm-to-farm were high, backyard farms could also a potential source for HPAIV transmission to commercial poultry farms.
The combined influence of body size and density on cohesive sediment resuspension by bioturbators
Cozzoli, Francesco ; Bouma, Tjeerd J. ; Ottolander, Pauline ; Lluch, Maria Salvador ; Ysebaert, Tom ; Herman, Peter M.J. - \ 2018
Scientific Reports 8 (2018)1. - ISSN 2045-2322
We propose an empirical framework to scale the effects of bioturbation on sediment resuspension to population bioturbation activity, approximated as population metabolic rate. Individual metabolic rates have been estimated as functions of body size and extrapolated to population level. We used experimental flumes to test this approach across different types of marine, soft-sediment bioturbators. We observed that a large part of the variance in biota-mediated sediment resuspension can be explained by a positive relationship with population metabolic rate. Other mechanisms can strongly influence the outcome, such as bioturbation of deep sediment strata, biotic interactions with hydrodynamic stress and overlapping areas of influence must be further investigated. By relating the biota-mediated changes in resuspended sediment to metabolism, we can place our observations within the broader context of the metabolic theory of ecology and to formulate general expectations about changes in biota-mediated sediment resuspension in response to changes in population structure and climate change.
Exposure of coastal ecosystems to river plume spreading across a near-equatorial continental shelf
Tarya, A. ; Hoitink, A.J.F. ; Vegt, M. van der; Katwijk, M.M. van; Hoeksema, B.W. ; Bouma, T.J. ; Lamers, L.P.M. ; Christianen, M.J.A. - \ 2018
Continental Shelf Research 153 (2018). - ISSN 0278-4343 - p. 1 - 15.
Coral reef - Exposure risk - Hydrodynamic model - River plume - Seagrass
The Berau Continental Shelf (BCS) in East Kalimantan, Indonesia, harbours various tropical marine ecosystems, including mangroves, seagrass meadows and coral reefs. These ecosystem are located partly within reach of the Berau River plume, which may affect ecosystem health through exposure to land-derived sediments, nutrients and pollutants carried by the plume. This study aims (1) to assess the exposure risk of the BCS coastal ecosystems to river plume water, measured as exposure time to three different salinity levels, (2) to identify the relationships between these salinity levels and the abundance and diversity of coral and seagrass ecosystems, and (3) to determine a suitable indicator for the impacts of salinity on coral reef and seagrass health. We analysed hydrodynamic models, classified salinity levels, and quantified the correlations between the salinity model parameters and ecological metrics for the BCS systems. An Empirical Orthogonal Functions (EOF) analysis revealed three modes of river plume dispersal patterns, which strongly reflect monsoon seasonality. The first mode, explaining 39% of the variability, was associated with the southward movement of the plume due to northerly winds, while the second and third modes (explaining 29% and 26% of the variability, respectively) were associated with the northeastward migration of the plume related to southwesterly and southerly winds. Exposure to low salinity showed higher correlations with biological indicators than mean salinity, indicating that low salinity is a more suitable indicator for coastal ecosystem health. Significant correlations (R2) were found between exposure time to low salinity (days with salinity values below 25 PSU) with coral cover, coral species richness, seagrass cover, the number of seagrass species, seagrass leaf phosphorus, nitrogen, C:N ratio and iron content. By comparing the correlation coefficients and the slopes of the regression lines, our study suggests that coral reefs are more susceptible to low salinity levels exposure than seagrass meadows. Regarding the risk of corals being exposed to low salinity, nearshore and northern barrier reefs were classified as “high risk” the middle barrier reef as “medium to high risk” and southern barrier reefs as “medium risk”. Further offshore, the oceanic reefs were classified as “low risk”. Regarding the seagrass meadows, the nearshore region was categorized as “high risk” the barrier reef as “medium to low risk” and oceanic reefs as “low risk”. This study contributes to assessing the potential impacts of salinity on the BCS ecosystems, and further provides a knowledge base for marine conservation planning.
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